It likely has to do with whether the iterative calculation for PTC and the self-employed health insurance deduction described in IRS Pub 974 converges to a stable result. The deduction for self-employed retirement contributions changes AGI, affecting the iterative PTC calculation. From $2,999 and $3,001 the calculation apparently converges to a stable result while for $3,000 it does not and TurboTax defaults to a more conservative result that lowers your refund.
